Testing for a wildlife reservoir of divergent SARS-CoV-2 in white-tailed deer
Authors: Crawshaw, L., J. D. Kotwa, S. P. Jeeves, C. Loomer, A. Dibernardo, A. Stewart, S. L. Newar, E. Chien, W. Yim, P. Kruczkiewicz, O. Vernygora, O. Lung, A. I. Schulte-Hostedde, L. Nituch, F. Maguire, B. Pickering, C. M. Jardine, H. Coatsworth, S. Mubareka, and J. Bowman
The 2021 discovery of a divergent lineage (B.1.641) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in free-ranging white-tailed deer (Odocoileus virginianus) in Ontario raised concerns that deer were a potential reservoir. To assess whether B.1.641 was still circulating in deer and to test for cross-species spillover, we established a surveillance program in Ontario by sampling wildlife via existing ecological projects and through active surveillance of captive and wild animals. Between 2022 and 2024, we tested 2839 animals, identifying one active SARS-CoV-2 infection in a deer (likely a spillover event involving a recombinant XBB.2.3.11.3 lineage), but no cases of B.1.641. Overall, 93 wild animals (6.8%) tested positive for antibodies, including 89 white-tailed deer, two Virginia opossums (Didelphis virginiana), one American mink (Neogale vison), and one river otter (Lontra canadensis). In southwestern Ontario, where B.1.641 was originally detected, 15.2% of deer samples were seropositive. Generalized Linear Models demonstrated that seropositive deer were more likely to be in areas with a higher fall deer harvest and human population, and closer to previous B.1.641 cases. Our data suggest that deer-associated B.1.641 may have caused a relatively localized epizootic without forming a stable reservoir. This study underscores the importance of One Health-focused surveillance.